# Force-Field Parameters
gromacs            on
grotopfile         my_topology_02.top
coordinates        dmpc_npat.pdb
                                                                                                                                                             
set temp           303.15  ;# target temperature used several times below
                                                                                                                                                             
# Periodic Boundary conditions
cellBasisVector1    61.760     0.   0.  ;# vector to the next image
cellBasisVector2     0.   61.760    0.
cellBasisVector3     0.    0   66.608
cellOrigin           0.    0.   0.  ;# the *center* of the cell
# the z dimension is going to shrink so pad sufficiently
# the margin could be reduced once the cell is equilibrated
margin 5

temperature	0

outputEnergies	100
outputTiming	500

binaryrestart   yes
restartfreq     500
xstFreq		100
dcdFreq		100

dcdUnitCell     yes
wrapAll		on
wrapNearest	on

timestep	1
nonBondedFreq	1
fullElectFrequency 1
stepsPerCycle	10 #20

switching	on
switchDist	8.5
cutoff		10	
pairlistdist	11.5

Pme		yes
PmeGridsizeX    64
PmeGridsizeY    64
PmeGridsizeZ	64	

exclude		scaled1-4
1-4scaling	1.0

#fixedAtoms		on
#fixedAtomsForces	on
#fixedAtomsFile		fix_backbone.pdb
#fixedAtomsCol		B

#constraints	on
#consRef		restrain_ca.pdb
#consKFile	restrain_ca.pdb
#consKCol	B

langevin		on
langevinDamping		10
langevinTemp		$temp
langevinHydrogen	off

langevinPiston		on
langevinPistonTarget	1.01325
langevinPistonPeriod	200
langevinPistonDecay	100
langevinPistonTemp	$temp

useGroupPressure	no	# smaller fluctuations
useFlexibleCell		yes	# allow dimensions to fluctuate independently
useConstantArea 	yes	# fix shape in x-y plane

#binaryoutput	off
outputname	mini-heat

# run one step to get into scripting mode
minimize 0

# turn off until later
langevinPiston	off

# minimize nonbackbone atoms
#minimize 1000
#output min_fix

# min all atoms
#fixedAtoms	off
#minimize 10
#output step01-min_all

# heat with CAs restrained
# langevin	on
run 10
output step02-heat

# equilibrate volume with CAs restrained
langevinPiston	on
run 10
output step03-equil

# equilibrate volume without restraints
#constraintScaling	0
run 10